User:Eric Martz/Sandbox 2





At left is a scene obtained in FirstGlance in Jmol, using the Contacts dialog. The state script was generated by Jmol 11.5.35, the same version that was in use in Proteopedia when this page was created.

Here is the scene obtained when the state script is run in Jmol within Proteopedia. The only change made to the state script was that the "load" command was commented out. The relevant PDB file, 2hhd, was already loaded in Proteopedia's Scene Authoring Tool before the state script was executed. (I opened the SAT, loaded 2hhd, opened the Jmol console, pasted in the script and executed it, then saved the scene.)

The only problem is that the cartoon was not turned off by the state script. This appears to be a problem in Jmol: I can reproduce it when I paste the state script into Jmol in FirstGlance, provided that the "load" command is commented out.

Here is the result after  select protein; cartoon off.

Finally, I tried loading the molecule into the SAT, then using the SAT to select all, hide selected. Now I had a blank white Jmol. Then I excecuted the state script, producing this result.

In short, this strategy appears to work well!